[Bioc-devel] Seqlengths not set in TxDb.Athaliana.BioMart.plantsmart19

Hervé Pagès hpages at fhcrc.org
Tue Jul 1 03:21:07 CEST 2014

Hi Vince,

On 06/26/2014 11:55 PM, Vince S. Buffalo wrote:
> I was surprised to see that sequence lengths weren't set in the
> transcriptDb object TxDb.Athaliana.BioMart.plantsmart19 (I
> checked TxDb.Athaliana.BioMart.plantsmart21 in devel too, and it had the
> same issue). This seems like something that would be set (though maybe
> TranscriptDb objects created from BioMart don't automatically receive this
> information?). Is this something that could be set in future versions?

Problem is that the makeTranscriptDbFromBiomart() function (which is
used to generate these TxDb packages) didn't know how to extract the
sequence lengths from the Ensembl Plants db so far. One difficulty
AFAIK is that this cannot be done via the BioMart interface so this
information has to be retrieved directly from the underlying db.

This now works in GenomicFeatures 1.17.12 (devel):

   txdb <- makeTranscriptDbFromBiomart("plants_mart_21", 


   > seqlengths(txdb)
          1        2        3        4        5       Mt       Pt
   30427671 19698289 23459830 18585056 26975502   366924   154478

The TxDb.Athaliana.BioMart.plantsmart21 package in devel will also
get the sequence lengths when we re-generate it but this will only
happen a few weeks before the BioC 3.0 release (and at that time it
might become TxDb.Athaliana.BioMart.plantsmart22).


> Vince

Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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